Basilar trunk saccular aneurysms associated with fenestration are infrequent, especially in the middle or distal portion of the basilar artery. Surgical treatment of the basilar trunk aneurysm is difficult, due to its anatomical environment and the complicated surgical exposure. A 46-year-old woman presenting with Hunt and Kosnik grade II subarachnoid hemorrhage was found to have a ruptured aneurysm arising at the proximal corner of the associated fenestration in the middle portion of the basilar artery. Because of surgical difficulties anticipated in approaching the aneurysm, it was decided to treat it with endovascular embolization utilizing the Guglielmi detachable coil; and complete occlusion of the aneurysm was obtained. The efficacy of endovascular treatment for the basilar trunk aneurysm with associated fenestration is discussed from anatomical and embryological points of view, and relevant literature is reviewed.